Extinction and the ESA

Abstract

The success of the Endangered Species Act is often measured by comparing the number of species declared extinct to the number of listed species, which indicates success on the order of 99%. Here we check that measure against the discussions of extinction by the Fish and Wildlife Service and the National Marine Fisheries Service by computationally mining five-year status reviews. We find that 81 (~5%) ESA-listed species are known to be or are likely to be extinct. The extinctions are concentrated in Hawaii and a swath that extends from Mississippi to Virginia.

The extinction crisis of the modern era was a key motvation for the ESA: the goals of the law include preventing extinction and recovering species so they are no longer threatened with extinction. One of the ways ESA success is measured is by comparing the number of listed species to the number that are extinct. As of this writing, ten species have been removed from the list of threatened and endangered species, and the list includes 1,652 species. Those numbers suggest 99.4% of species have been saved by the ESA, which is a great accomplishment.

But there are a few problems with using the number of species “delisted due to extinction” as the metric of success. First, it ignores the key goal of species recovery and uses the lower bar of mere existence as success. But we don’t want to argue that plants and animals known only to exist in captivity count as successes. Success is wildlife out in their homes on the landscape.

Second, we know that the ten delisted species are simply the ones formally accepted as extinct. But proving extinction is tough; we have too many examples where a species hadn’t been seen for many, many years–multiple decades and even over a century–only to be rediscovered. For such reasons, declarations of extinction are a rare occurrence. At the same time, we often have a very good idea that well-documented species are really-and-truly extinct. We hold off on the declarations of extinction and the removal of protections because of the small but real chance that one or a few individuals still exist.

Here we identify the species that experts - biologists with the U.S. Fish and Wildlife Service (FWS) and National Marine Fisheries Service (NMFS; collectively, the Services) - have good reason to believe are or may be extinct. Declaring extinction may not be warranted for many or most of these, but these professionals have indicated that extinction is likely to some greater or lesser degree. Getting a better handle on the number of species thought to be extinct rather than relying on the number delisted due to extinction is an important first step in thoroughly understanding the effectiveness of the ESA.

Identifying possible/probable extinctions

The first question we address is how many species are extinct. Pinning down that number is tricky because extinction is fundamentally hard: one can’t prove absence the same way we prove presence. Rather than a declaration of extinct, we set the bar at a level of experts’ statements that they think the species is or may be extinct. We mined the text of all ~1,400 five-year status reviews, totalling >30,000 pages, we need to find a relatively small number of phrases that indicate extinction.

This search returned 387 matches to the set of candidate phrase patterns, including patterns that indicate a higher likelihood of extinction such as:

  • in november and december of 2006, a visual and acoustic survey failed to locate a single baiji leading to conclusions that the baiji is likely extinct (turvey 2008; turvey et al.
  • 1.3.4 review history monk seal 5-year review: november 9, 1984 a caribbean monk seal 5-year review published on november 9, 1984, determined that the best available information indicated the caribbean monk seal is extinct.
  • based upon our review of the status of this species, we conclude that the caribbean monk seal is extinct, primarily due to human exploitation.
  • 3.3 listing and reclassification priority number: _ 1 delisting priority number: 6 1 4.0 recommendations for future actions this status review concludes the caribbean monk seal is extinct.
  • the caribbean monk seal is extinct.
  • by the early 1980’s, palos verdes blue butterflies were found at only 10 locations (arnold 1987), and none were observed between 1983 and 1993, leading to the conclusion that the palos verdes blue butterfly was likely extinct (arnold 1987; mattoni 1992).
  • gary vinyard (1984), which attributed this extinction to limited distribution, habitat disturbance, and introductions of nonnative fishes.
  • a project has been funded by a service endangered species act section 6 grant to develop a protocol to estimate san diego fairy shrimp population sizes and conduct population viability analyses in real time, in order to detect a decline preceding the likely extinction of a population.
  • this taxon has not been collected in more than 70 years and is likely extinct.
  • 2.3.1.5 spatial distribution, trends in spatial distribution (e.g. increasingly fragmented, increased numbers of corridors, etc.), or historic range (e.g. corrections to the historical range, change in distribution of the species’ within its historic range, etc.): -4- ^l at the time it was listed, the little mariana fruit bat had last been observed in the 1960s, and the species has been considered as likely extinct since the time of the recovery plan’s publication in 1990.

Perusing the pattern matches, we find (as expected) both true positives (i.e., the meaning of the matched sentence comports with the idea we have in mind) and false positives (e.g., local extinctions or species previously believed extinct but since re-discovered). To ensure we are working with the right numbers, we manually checked each 5-year review with an extinction phrase match to remove the false-positives.

From the manually filtered data we find 37 species that are believed extinct to some greater or lesser degree, plus the snail genus Achatinella (see below).

Acaena exigua
Achatinella spp.
Akialoa stejnegeri
Amaranthus brownii
Anolis roosevelti
Cyanea copelandii ssp. copelandii
Cyanea superba
Cyrtandra crenata
Dipodomys heermanni morroensis
Eleutherodactylus jasperi
Epioblasma torulosa torulosa
Erimystax cahni
Etheostoma sellare
Hemignathus hanapepe
Hibiscadelphus woodii
Kadua degeneri
Loxops ochraceus
Melamprosops phaeosoma
Melicope quadrangularis
Moho braccatus
Myadestes lanaiensis rutha
Myadestes myadestinus
Numenius borealis
Obovaria retusa
Ochrosia kilaueaensis
Paroreomyza flammea
Paroreomyza maculata
Phyllostegia glabra var. lanaiensis
Phyllostegia mollis
Pleurobema curtum
Pleurobema marshalli
Polygyriscus virginianus
Psittirostra psittacea
Pteropus tokudae
Puma (=Felis) concolor couguar
Quadrula stapes
Tetramolopium capillare
Zosterops conspicillatus conspicillatus

(Note this does not include species that are extinct in the wild, but often number just a few in propagation or captivity. We identified 6 such species in our scans - Delissea rhytidosperma, Hibiscadelphus giffardianus, Phyllostegia kaalaensis, Cyanea superba, Rallus owstoni, Hibiscadelphus hualalaiensis - but the number is likely higher.)

Together with the ten species that have been delisted due to extinction, 81 (5%) current or formerly ESA-listed species are thought, to some greater or lesser extent, to be extinct.

Most of the extinct species are from Hawaii, with many that are plants Box 1 or snails Box 2. Note that we collapse all 31 extinct species in the genus Achatinella to “Achatinella spp.” in subsequent analyses because they were all from the same place and faced the same threats. To count them individually when trying to understand broad patterns related to extinction would bias our inferences.

Geography of extinctions

The next question is where the extinctions have occurred. Hawaii, of course, tops the list, but where are the other species?

States with the most (likely) extinctions.

Again, Hawaii clearly shows up with the most species, but the swath from Mississippi to Virginia stands out too. Most of these species are mussels and fish, so the issue could be related to the problems apparent in this (albeit old) Clean Water Act 303(d) impaired waters map:

Impairment as measured by EPA standards is not the complete answer why are extinctions not higher in other states with realtively high impairment.

state n
Hawaii 24
Alabama 4
Mississippi 4
Guam 3
Tennessee 3
Virginia 3

In addition to the state-level patterns of extinction, we can use counties of occurrence to evaluate patterns of the geography of extinction. The ten counties with the most extinct species include:

State, County n
Honolulu, Hawaii 8
Kauai, Hawaii 7
Maui, Hawaii 7
Hawaii, Hawaii 5
Guam, Guam 3
Bedford, Tennessee 2
Bland, Virginia 2
Blount, Tennessee 2
Buchanan, Virginia 2
Butler, Kentucky 2

As expected, Hawaiian counties top the list, followed by Guam, then southern Appalachian counties in Tennessee, Virginia, and Kentucky. Thus, although Alabama and Mississippi have more extinct, listed species than these states, those species are (were) more concentrated in Tennessee, Virginia, and Kentucky.

Common threats and habitats

Given the list of likely extinct species, we would like to know what they have in common. Any commonalities might help inform prioritization efforts that can stem future extinctions. We build off of the data available through the IUCN’s Red List database.

Habitats

habitat n
NA 21
Forest - Subtropical/Tropical Moist Montane 11
Forest - Subtropical/Tropical Moist Lowland 8
Forest - Subtropical/Tropical Dry 6
Wetlands (inland) - Permanent Rivers/Streams/Creeks (includes waterfalls) 3
Rocky areas (eg. inland cliffs, mountain peaks) 2
Grassland - Subtropical/Tropical Dry 1
Grassland - Tundra 1
Marine Coastal/Supratidal - Sea Cliffs and Rocky Offshore Islands 1
Wetlands (inland) - Bogs, Marshes, Swamps, Fens, Peatlands 1

The most common defined habitats for the extinct species parallels those species’ geography: subtropical / tropical forests of Hawaii where species such as the Achatinella snails, various plants, and birds lived. Inland wetlands, in particular the rivers, streams, and creeks inhabited by likely extinct mussels and fishes, are the second major group. Last, notice the most common habitat type is actually “NA.” This points to a limitation of the IUCN’s database - incomplete information - that we will propose to help address in another venue.

Threats

title n
Invasive non-native/alien species/diseases 22
Unspecified species 22
Invasive non-native/alien species/diseases (Sus domesticus) 14
Named species (Sus domesticus) 14
NA 14
Named species 11
Livestock farming & ranching 9
Logging & wood harvesting 7
Annual & perennial non-timber crops 6
Fire & fire suppression 6
code n
8.1 90
8.1.2 74
8.1.1 20
NA 14
2.3 9
5.3 7
2.1 6
5.3.3 6
7.1 6
11.1 5

Box 1. Complementary data from PEP

The Plant Extinction Prevention (PEP) Program works exhaustively to monitor and conserve Hawaiian plants. They also provide more up- to-date data on the status of many imperiled plants than FWS documents, and should probably be considered authoritative for PEP species.

We downloaded the 2017-03-16 list from PEP’s website then used Adobe’s online extraction service to render the tables as a spreadsheet for processing. To begin, we have a high-level overview of how PEP classifies the covered species:

PEP_class n
N/A 1
PEP 227
PEP-Extinct in Wild 14
PEP-EXTINCT? 20
PEP-EXTIRPATED 45
PEP-Extirpated in Wild 3
PEP-EXTIRPATED? 14

Appropriately, PEP uses “?” to denote species for which extirpation and extinction are unknown. The refinement of extinct in the wild vs. extinct from the planet is also useful to consider. Last, in addition to the extinctions, the PEP data highlight the problem of extirpations: 34 PEP species have been (or probably have been) extirpated from one or more of the islands. First, the number of extirpations by island:

extirpations
Maui 14
Molokai 14
Lanai 10
Kauai 7
Oahu 5
Hawaii 4
Niihau 4
Kahoolawe 1

And second, by most species:

extirpations
Scaevola coriacea 5
Adenophorus periens 4
Diplazium molokaiense 4
Isodendrion pyrifolium 4
Canavalia pubescens 3
Acaena exigua 2
Asplenium dielerectum 2
Brighamia rockii 2
Deparia kaalaana 2
Gardenia brighamii 2

The PEP data adds depth to our understanding of extinctions and extirpations among Hawaiian plants, but PEP doesn’t cover all ESA-listed plants. By combining PEP table with county occurrence data, we find 320 species are not covered by PEP; more are missing than are covered by PEP. For these species in particular it is important for FWS to track species status. One way that is done is with ESA-mandated five-year reviews of species status.

There are 279 non-PEP species with 5-year reviews available, and of those reviews, 200 are out-of-date (i.e., more than five years old).

Box 2. Achatinella snails

Some 43 species of Achatinella snails have been described, all native to the tropical forests of Oahu. Unfortunately, they have suffered more likely extinctions than any other genus of ESA-listed species. Here we summarize the status as given in the last five-year review for the genus (2011) plus status information gleaned from other sources (e.g., IUCN and NatureServe).

Among the 43 Achatinella, current publicly available information indicates 33 are extinct:

species year_most_recent_info year_last_observed
Achatinella abbreviata 2009 1963
Achatinella apexfulva_cestus 2009 1966
Achatinella apexfulva_leucorraphe 2011 1989
Achatinella apexfulva_vittata 2011 1953
Achatinella bellula 2011 1981
Achatinella buddii 2011 1900
Achatinella bulimoides 2011 2009-2011
Achatinella bulimoides_elegans 2011 1952
Achatinella bulimoides_rosea 2011 1949
Achatinella caesia 2011 1900
Achatinella casta 2011 NA
Achatinella curta 2011 1989
Achatinella decora 2011 1900
Achatinella dimorpha 2011 1967
Achatinella juddii 2011 1958
Achatinella juncea 2011 NA
Achatinella lehuiensis 2011 1922
Achatinella lorata 2011 1979
Achatinella papyracea 2011 NA
Achatinella phaeozona 2011 1974
Achatinella pulcherrima 2011 1993
Achatinella pupukanioe 2011 1980
Achatinella spaldingi 2011 1938
Achatinella stewartii 2011 1963
Achatinella swiftii 2011 1970
Achatinella taeniolata 2011 1966
Achatinella thaanumi 2011 1900
Achatinella turgida 2011 1974
Achatinella valida 2011 1951
Achatinella viridans 2011 1979
Achatinella vulpina 2011 1965

Methods

Patterns

We used a set of seven regular expression patterns as a coarse filter:

  1. "(possibly|may be|have become) extinct"
  2. "(certainly being|probably|is|likely|probably being) extinct"
  3. "no (populations|individuals)( are)* known"
  4. "no( known| living)* individuals"
  5. "extinct in( the)* wild"
  6. "last (seen|observed|found) in [0-9oOiI]+"
  7. "functionally extinct"

In these patterns, “|” means “or” for the set of words inside parentheses. For example, the first pattern would match “possibly extinct,” “may be extinct,” or “have become extinct.” The “*" means the preceding letter or word matches zero or more times, whereas “+” means the preceding word/letter(s) must match one or more times. We checked all seven patterns against all 1,385 five-year reviews we collected from ECOS and NMFS’s recovery site.